The OsNAC41-RoLe1-OsAGAP module promotes root development and drought resistance in upland rice.

Drought is a major environmental stress limiting crop yields worldwide. Upland rice (Oryza sativa) has evolved complex genetic mechanisms for adaptative growth under drought stress. However, few genetic variants that mediate drought resistance in upland rice have been identified, and little is known about the evolution of this trait during rice domestication. In this study, using a genome-wide association study we identified ROOT LENGTH 1 (RoLe1) that controls rice root length and drought resistance. We found that a G-to-T polymorphism in the RoLe1 promoter causes increased binding of the transcription factor OsNAC41 and thereby enhanced expression of RoLe1. We further showed that RoLe1 interacts with OsAGAP, an ARF-GTPase activating protein involved in auxin-dependent root development, and interferes with its function to modulate root development. Interestingly, RoLe1 could enhance crop yield by increasing the seed-setting rate under moderate drought conditions. Genomic evolutionary analysis revealed that a newly arisen favorable allelic variant, proRoLe1, originated from the midwest Asia and was retained in upland rice during domestication. Collectively, our study identifies an OsNAC41-RoLe1-OsAGAP module that promotes upland rice root development and drought resistance, providing promising genetic targets for molecular breeding of drought-resistant rice varieties.